The recruitment of scallops (and beyond) by two different artificial collectors (Gulf of Taranto,Mediterranean Sea)

This study provides for the first time an evaluation of the natural availability of scallop seeds along the coastal area of Taranto (Mediterranean Sea, Southern Italy). To select the best artificial collectors to harvest scallop seeds in this area, cylindrical collectors (Cyl) were compared to traditional ‘Japanese‐style onion bags’ (Bag) across three sites. Scallops represented 26.6% of total bivalve recruitment among all collectors (782 ± 331 ind. m^?2). The most recruited scallops were Flexopecten glaber and Mimachlamys varia. The white (F. glaber) and black scallops (M. varia) were abundant at all three sites, while the queen scallop, Aequipecten opercularis, was only found at one site. Beyond the recruitment of scallops, numerous other potential commercial bivalve species were collected, including Limaria tuberculata, which was the most abundant bivalve species (33.3% of total recruitment). At all sites, Bag collectors had higher recruitment than Cyl collectors. Scallops recruited in artificial collectors exhibited a multicohort size distribution at most sites, suggesting potentially continuous reproductive activity in the scallop populations. F. glaber, M. varia and L. tuberculata could be good candidates to diversify the aquaculture production because of the availability of seed and their growth rate. Moreover, the farming of these bivalves integrates well with other forms of aquaculture (e.g. mussels), thus potentially offering farmers an additional source of income.     

Experimental collection of great scallop postlarvae and other benthic species in the Bay of Brest: settlement patterns in relation to spatio-temporal variability of environmental factors

Settlement patterns of great scallop (Pecten maximus) postlarvae and other benthic species in the Bay of Brest were studied from 2-D and 3-D collectors to clarify biotic interactions at the postlarval stage. Plane tiles became colonized mainly by epifaunal suspension feeders, while the 3-D substrata collected a more diverse fauna. Both species diversity and total abundance were higher in Netlon bags, compared with sandstone tiles. However, hydroids, bryozoans, tubicolous polychaetes, a number of epifaunal molluscs and macroalgae were more abundant on tiles. Between-sites differences in taxonomic group abundances mostly reflected the benthic fauna and flora beneath the collectors and would be explained by differential settlement and survival, according to local environmental conditions. Sediment type, depth, salinity, water turbulence, food and biotic interactions would be the factors regulating settlement. Bryozoans, hydrozoans, Anomia ephippium, Crepidula fornicata, mussels, tubicolous polychaetes, Pisidia longicornis, Hiatella arctica, Aequipecten opercularis and Chlamys varia were the main potential competitors of Pecten maximus collected. Crabs and Nassaridae would account for most of the potential scallop predators. Possible ways of improving scallop spat collection and cultivation are discussed with reference to the efficiency and placement of collectors, to environmental characteristics and to the intensity of biotic interactions at the postlarval stage.     

Study of seasonal settlements of five scallop species in the western Mediterranean

Scallop settlements were examined over a 16 month period using collectors placed in the sea at 28 day intervals near Torre la Sal Beach, Castellón, Eastern Spain in the western Mediterranean. Collectors were set over depths of 20 m and five species, Flexopecten flexuosus, Chlamys varia, Aequipecten opercularis, Pecten jacobaeus and Palliolum incomparabile, were collected. The most frequent species, F. flexuosus, had peak settlements in August 1992 and in July 1993. C. varia had peaks in April and July 1992 and in June 1993. Both of these species settled throughout the year, except in winter. A. opercularis settled predominantly from February to June and in October, but with a few settlements during the rest of the year. Pecten jacobaeus had a small peak in February and another peak from April to July. P. incomparabile spat were rare. Settlements were studied in relation to chlorophyll a, suspended particulate and sea temperature data in the area of study.     

Perkinsus mediterraneus infection induces oxidative stress in the mollusc Mimachlamys varia

Perkinsus mediterraneus is a protozoan parasite that can cause marine mollusc diseases known as perkinsosis being a serious threat for clam cultures worldwide. The aim of the present study was first to determine the Perkinsus species infecting the variegated scallop Mimachlamys varia and then to evaluate the existence of oxidative stress in gills of M. varia according to different degrees of infection. DNA sequencing confirmed that P. mediterraneus was the species infecting M. varia. ROS production was progressively increasing with the degree of infection although the differences were only significant in the high-infected group. Low degree of infection significantly increased superoxide dismutase (SOD) and glutathione S-transferase (GST) activities and nitrite levels with respect to the control group. In the high-infected group, a significant increase was evidenced in all analysed enzymes, catalase, SOD, glutathione reductase and GST. Non-significant differences in MDA levels were observed between the control and low-infected groups; however, a significant increase in MDA levels was observed in the high-infected group. In conclusion, the infection by Perkinsus mediterraneus in M. varia induces oxidative stress and an antioxidant response directly related to the infection degree that can contribute to the pathogenicity of the infection.     

Mugil curema in Argentinean waters: Combined morphological and molecular approach

A previously unidentified mullet species (Mugil sp.) from Mar Chiquita lagoon, Argentina, was compared with two candidate species Mugil curema and M. cephalus using 12 truss landmarks and three mitochondrial DNA genes (12S rRNA, cytochrome b and COI). Both procedures confirmed that the Argentinean fish were white mullet M. curema. Morphological comparisons clearly segregated M. curema from M. cephalus samples in PCA plot. Similarly, Argentinean haplotypes at each gene overlapped with M. curema reference samples while M. cephalus haplotypes remained distinct. These combined data provide a valuable baseline for further investigations on the geographic distribution of this commercially important species group.     

Polymerase chain reaction-restriction fragment length polymorphism analysis for species identification of hairtail fish fillets from supermarkets in Japan

Hairtail fillets are marketed as both fresh and frozen forms in retail outlets within Japan. The present study was undertaken to develop a rapid and reliable method for identification of the hairtail species in commercial fillets. A total of 64 fillet samples, caught from various localities within Japan and purchased from various supermarkets, were analyzed. Polymerase chain reaction (PCR) amplification of a portion of the mitochondrial DNA encoding 16S ribosomal RNA gene and subsequent restriction digestion of the amplified products, using Vspl endonuclease, generated different restriction patterns indicating two different species of hairtails in the fillet samples. The results indicated that the commercial hairtail fillets, labeled and marketed as ‘Tachiuo’ in Japan, were comprised of two species of hairtails with Trichiurus japonicus (commonly called Tachiuo) accounting for 47% and Trichiurus sp. 2 (commonly called Tenjikutachi) accounting for 53% of the analyzed samples. This simple and inexpensive PCR-restriction fragment length polymorphism analysis can be routinely applied to determine species composition of hairtails in commercial fillets.     

Estimating fishery effects in a marine protected area: Lamlash Bay

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Genetic identification and phylogenetic inferences in different Mugilidae species using 5S rDNA markers

A DNA methodology was developed to discriminate fry of six Mugilidae species found in the Mediterranean, namely Mugil cephalus, Mugil so‐iuy, Chelon labrosus, Liza aurata, Liza ramada and Liza saliens. Polymerase chain reaction (PCR) amplification of the 5S rDNA gene was used for the identification of the above six species. PCR products of two species showed different patterns on EtBr‐stained agarose gels; M. so‐iuy gave a pattern of three bands, while L. saliens gave a pattern of one band. Mugil cephalus, C. labrosus, L. aurata and L. ramada gave a pattern of two bands. Subsequent sequencing analyses revealed unique haplotypes for each of the remaining four species. This is a genetic technique that could be applied in hatcheries, for identification of fry mullet's species. Furthermore, 5S rDNA sequences of each of five of the studied species (i.e. M. cephalus, C. labrosus, L. aurata, L. ramada and L. saliens), as well as a sequence of Oedalechilus labeo that belongs to the Mugilidae family, were aligned and used for the examination of the phylogenetic relationships among them. Phylogenetic trees produced in our study are in general agreement with those presented in the literature. This is the first study to use a nuclear marker to elucidate the phylogeny of Mugilidae species.     

Genetic population structure of harbour seals in the United Kingdom and neighbouring waters

1. In the United Kingdom (UK), several harbour seal (Phoca vitulina) populations have been declining over the past decade. In order to understand the effect of these changes in abundance, this study seeks to determine the population structure of harbour seals in the UK, and in Scotland in particular, on a wider and finer spatial scale than has previously been reported.
2. Harbour seals were genotyped from 18 different localities throughout the UK and neighbouring localities in mainland Europe, at 12 microsatellite loci. Results from Bayesian and frequency based tests of population structure suggested an initial structural division into two main groups consisting of localities in northern UK and southern UK–mainland Europe, respectively.
3. These two clusters were further divided into four geographically distinct genetic clusters.
4. An overall agreement between the genetic results and the existing management areas for UK harbour seals was observed, but it is also clear that an adaptive management approach should be adopted, in which the delineation of the current management areas is maintained until further genetic and ecological information has been accumulated and analysed.

     

Patterns and impacts of fish bycatch in a scallop dredge fishery

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我国五大湖日本沼虾线粒体COI基因部分片段序列比较

对我国五大湖日本沼虾100个野生个体的线粒体细胞色素氧化酶亚基I（COI）部分序列进行了测定和分析，经比对获得578bp核苷酸片段，发现49个变异位点，得到35个单倍型，包括7个共享单倍型，各群体都具有较好的单倍型多态性和核苷酸多态性，其中鄱阳湖群体遗传多样性相对最高。AMOVA分析表明，五群体间总遗传分化系数F_st＝0.31873 （P<0.05）， 群体间具有较高的遗传分化。MEGA3.1软件计算五群体的Kimura 2-paramter遗传距离，洞庭湖群体和巢湖群体之间的遗传距离最远为0.0191，巢湖群体和洪泽湖群体之间的遗传距离最近为0.0051。以同属胖掌沼虾（Macrobrachium inflatum）为外群分别构建了NJ和UPGMA系统树，结果显示洞庭湖和鄱阳湖为一族群，太湖、巢湖和洪泽湖为一族群。     

Hydrodredge: Reducing the negative impacts of scallop dredging

Scallop dredges typically use teeth or a cutting bar to dig though the sediment and are associated with detrimental impacts on marine benthos. A low-impact ‘Hydrodredge’ was tested that uses ‘cups’ to deflect water downward in a turbulent wave sufficient to lift scallops from the seabed. Trials took place in the Isle of Man fishery for great scallop (Pecten maximus) with the hydrodredge and a gang of local ‘Newhaven’ dredges towed simultaneously either side of a commercial scallop dredge vessel. When fished over three different ground types (smooth, medium and hard) and two tow-speeds (2.5 kt, 4.0 kt), the proportion of dead scallops and bycatch in the Hydrodredge was significantly less than in the Newhaven dredges. This result highlighted the role of the teeth on the tooth-bar in exerting severe (fatal) damage to the catch and bycatch. Rates of non-fatal damage to scallops and bycatch did not differ between gears, suggesting that such damage occurs as a result of contact with other parts of the gears such as the chain bag. The hydrodredge was less efficient at catching great scallops compared with the Newhaven dredges (10–40%). For great scallops, the cups did not significantly increase catch relative to the hydrodredge fished without cups, which contrasts with results for other surface-dwelling scallop species, e.g., Placopecten magellanicus and Aequipecten opercularis. Importantly, the Hydrodredge was designed in the New England fishery for giant scallop (P. magellanicus), a species typically lighter and less embedded than P. maximus and thus potentially more vulnerable to the flow patterns of the Hydrodredge.     

海湾扇贝南部亚种遗传多样性和选择特征的基因组学解析

为了探究海湾扇贝南部亚种(Argopecten irradians concentricus)的遗传多样性特征,通过全基因组重测序分析,系统解析了其群体遗传结构以及其与海湾扇贝北部亚种(Argopecten irradians irradians)间的遗传差异,共筛查出15059961个高质量单核苷酸多态性(single nucleotide polymorphisms,SNPs)位点。基于全基因组SNP的群体祖先成分推断、主成分分析和系统发生重构皆表明,南北亚种之间存在较为显著的遗传分化。其中,海湾扇贝南部亚种的近交水平和连锁不平衡程度更高。通过选择性清除分析,在海湾扇贝南部亚种中共鉴定出349个正选择基因,其中GHSR、HSF1、HABP2和Dna J等基因可能与其生长速度较快、耐热性较强以及免疫功能较强等环境适应性特征相关。该研究揭示了海湾扇贝亚种间遗传分化和选择特征,为扇贝的基因组研究和分子育种提供了数据支持。     

Novel decaplex PCR assay for simultaneous detection of scallop species with species‐specific primers targeting highly variable 5′ end of the 16S rRNA gene

Scallops (family Pectinidae) comprise species of high commercial value, supporting both commercial fisheries and mariculture activities. Accurate and reliable molecular methods for the species level identification are of outstanding utility for taxonomic and food authentication surveys. The mitochondrial 16S rRNA gene has been used to design species‐specific primers for identification of different bivalve species. However, the low interspecific variability at the 3′ end of this gene has limited its utility and only few scallop species have been assessed. In this study, we used the high variable 5′ end of the 16S gene to develop a novel decaplex PCR assay that enabled a fast and accurate identification of eight commercially important scallop species in a single PCR reaction. A total of 285 individuals including fresh and manufactured samples from eight different processed presentations from 11 different scallop species were collected representing diverse locations around the world. Our assay accurately identified all the analysed samples at the species level. Furthermore, to enhance the utility of our assay, the PCR product amplified by the family specific primer set that was utilized as positive control was also used for the identification of unknown (non‐target) scallop species by DNA sequencing analysis. In its present form, our multiplex PCR method can be of great utility for different types of studies involving scallop species and for research institutes and governmental agencies that regulate seafood authentication around the world.     

基于mtDNACytb基因序列的我国不同水系野生鲇种群遗传多样性与种群历史分析

为进一步了解鲇这一广布种的遗传多样性与种群遗传结构,阐明该经济鱼类的种群历史动态,本研究对我国长江(上游、中游)、珠江、福建、海南、辽河地区的野生鲇样本进行mtDNA Cytb基因序列测定与种群遗传多样性和遗传结构分析。结果显示,在所分析的216个序列样本中,共检测出78个单倍型,其中Hap_45在鲇不同群体中分布最为广泛;鲇总群体具有较高的单倍型多样性(Hd=0.948±0.009)和核酸多样性(Pi=0.017 99±0.000 55),暗示了其自然种群数量的相对稳定;单倍型系统发育与网络关系图分析显示,78种单倍型被分为4个分支,且不同单倍型分布相对集中,划分为4个谱系。中性检验与错配分析表明,不同水系野生鲇种群(4个谱系)在约晚更新世时期(0.04~0.05百万年)经历过近期种群扩张事件。     

我国近海星康吉鳗群体的形态学、遗传学比较研究

结合形态学、遗传学的方法,分别对青岛近海(黄海)、舟山近海(东海)的星康吉鳗群体做了相关系统的研究。通过单因素方差分析、判别分析、主成分分析方法对两个星康吉鳗地理群体的9个可量性状进行形态学比较研究;基于线粒体DNA (mtDNA)序列进行遗传学分析研究。形态学研究结果显示,舟山海域的星康吉鳗肌肉中含有"I"形硬肌间骨,青岛海域星康吉鳗的肌肉中无硬肌间骨;单因素方差分析结果显示,两个群体的7个可量指标:肛长、头宽、吻长、口裂长、眼径长、背鳍前长和胸鳍长存在显著差异;在主成分分析中,基于前两个主成分绘制的散点图基本能够将两个星康吉鳗群体区分开来;判别分析结果显示,青岛、舟山两群体的判别准确率分别为100%和94.7%。3种多元统计分析结果均表明青岛、舟山两个星康吉鳗群体在外部形态上存在一定程度差异,但根据75%识别与划分规则,认为两组群体的形态学差异尚未达到亚种水平。遗传学研究表明,在所检测的mtDNA水平上两个星康吉鳗群体遗传多样性无明显差异,邻接系统发育树未呈现明显的谱系关系,遗传分化指数FST也显示两群体遗传差异小,遗传分化不显著,属同一种群。     

Genetic variability of Austropotamobius italicus in the Marches region: implications for conservation

• 1. Ten populations of Austropotamobius italicus from the Marches region (Central Italy), two populations from the Appennines of Calabria and Basilicata (Southern Italy) and four populations from Friuli Venezia Giulia region were sampled to elucidate the geographical pattern of genetic variability in relation to recent and historical factors.
• 2. A total of nine COI haplotypes belonging to three separate lineages have been characterized. Both lineage A (Northern Marches region) and C (Friuli Venezia Giulia region) were represented by one haplotype and were related to the Istria 1 peninsula and SouthAlps/Western Balkans lineages respectively. The lineage B included seven haplotypes belonging to the Appenines lineage.
• 3. Two hypotheses on the origin of individuals belonging to the Istrian lineage in Marches are discussed: (i) a natural colonization from the Istria peninsula refugia by migrating westwards across the bridge between the Istria peninsula and Italy, (ii) an anthropogenic origin. Based on 16S rRNA sequences, the taxonomic status of lineage B and C, defined from COI mtDNA markers, belongs to A. i. meridionalis and that of lineage A belongs to A. i. carsicus. The existence of a complex geographic structure between Marches populations (Φst=0.66) of A. i. meridionalis should be further considered in conservation management. Copyright © 2010 John Wiley & Sons, Ltd.

     

Going,going, gone? Loss of genetic diversity in two critically endangered Australian freshwater fishes,Scaturiginichthys vermeilipinnis and Chlamydogobius squamigenus,from Great Artesian Basin springs at Edgbaston,Queensland, Australia

1. Artesian springs are particularly sensitive freshwater ecosystems, characterized by specialized flora and fauna which, owing to their isolation, are often endemic. Thus, protection of spring habitats and endemic spring biota is important for biodiversity conservation, particularly because human impacts such as invasive species, habitat destruction, and fragmentation can have such devastating effects.
2. This study investigated the mitochondrial DNA (mtDNA) genetic diversity and structure of two critically endangered (IUCN) freshwater fish species: red‐finned blue‐eye Scaturiginichthys vermeilipinnis, and Edgbaston goby Chlamydogobius squamigenus, with the aim of assisting management agencies to establish relocated populations that conserve the genetic integrity and evolutionary potential of both species.
3. 2862 bp from multiple mtDNA genes were amplified from 111 red‐finned blue‐eye individuals (17 from the 1990s and 94 from 2010), and a 660 bp segment of mtDNA cytochrome b was amplified from 111 Edgbaston goby individuals (from 2010). In total, 14 concatenated mtDNA haplotypes were identified in red‐finned blue‐eye and three cytb haplotypes were identified in Edgbaston goby.
4. Overall assessment of the genetic diversity and structure of the endemic fish fauna from the Edgbaston springs revealed low levels of diversity in both species and a loss of haplotypes in red‐finned blue‐eye over time. In addition, both species displayed significant genetic structure: at the spring scale for red‐finned blue‐eye and at the spring group scale for Edgbaston goby. It is concluded that without the appropriate management of relocated populations, such as considering genetic structure and diversity and selecting high quality habitats, these species are at a severe risk of losing evolutionary potential and becoming extinct. This study provides a valuable example for conservation managers of the contribution that population genetic studies can make regarding the adaptive management of endangered species.

Copyright © 2016 John Wiley & Sons, Ltd.